Microbial pathogens are becoming increasingly resistant to current antibiotics, limiting the availability of clinical treatment options for bacterial infections (1). It is imperative to develop novel classes of antibacterial compounds, preferably against a new target to avoid cross-resistance. Tuberculosis (TB) infects 9.6 million people a year and causes 1.5 million deaths each year (2). The problem presented by multi-drug resistance is illustrated by the 480,000 cases of multi-drug resistant TB (MDR-TB) that do not respond to first line treatment drugs, with around ten percent of these cases being extensively-drug resistant tuberculosis (XDR-TB) that are resistant to even some of the second line drugs (2, 3). New combinations of anti-TB drugs are needed to treat the MDR-TB and XDR-TB cases.
Topoisomerases are needed in every organism to regulate DNA topology so that vital cellular processes including DNA replication, transcription, recombination and repair can proceed without hindrance (4, 5). Type IIA topoisomerases cut and rejoin a double strand of DNA during catalysis (6). DNA gyrase and topoisomerase IV are prokaryotic type IIA topoisomerases that have been extensively explored as validated targets for antibacterial therapy in the clinic (7, 8). At least one type IA topoisomerase is present in every bacterial pathogen to resolve topological barriers that require the cutting and rejoining of a single strand of DNA and passage of DNA through the transient break (9). Topoisomerase I is the major type IA topoisomerase activity responsible for preventing excessive negative supercoiling in bacteria (10, 11). Bacterial topoisomerase I has received some recent interests as a novel antibacterial drug target (9, 12). Escherichia coli topoisomerase I (EcTopI) is the most extensively studied type IA topoisomerase, with crystal structures of covalent cleavage complex (13) and full-length enzyme-DNA complex (14) available. Inhibition of EcTopI by endogenous polypeptide inhibitors (15-17) can lead to cell killing even though compensatory mutations could allow E. coli strains with topA deletion to be viable (18, 19). There is also evidence that topoisomerase I function is essential for a number of bacterial pathogens including Streptococcus pneumoniae (20) and Helicobacter pylori (21). There is only one type IA topoisomerase encoded by the genomes of Mycobacteria. Mycobacterium tuberculosis topoisomerase I (MtbTop1) has been demonstrated in genetic studies to be essential for viability both in vitro (22, 23) and in vivo (23). Experimental data showed that the minimal inhibitory concentrations (MICs) of select small molecules against Mycobacterium tuberculosis can be shifted by overexpression of topoisomerase I (23, 24), further validating topoisomerase I as a vulnerable target in M. tuberculosis for chemical inhibition.
Many of the small molecules identified previously as bacterial topoisomerase I inhibitors are DNA intercalators (20, 24-26) or minor groove binders (27, 28) that would not be attractive candidates for antibiotics development. Therefore, there is an urgent need to develop compounds that target bacterial pathogen, in particular, through the inhibition of bacterial topoisomerase I.